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Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria meningitidis (monoclinic crystal form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KJJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 294 di-Potassium Hydrogen Phosphate 1.2 M, Sodium di-Hydrogen Phosphate 0.6 M, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.34 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.032 α = 90 b = 78.275 β = 103.62 c = 181.871 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2005-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.29 30 96.4 0.165 15 6.3 69756 -1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.37 90.6 0.996 2.2 5.8 6500
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KJJ 2.29 30 66128 3518 96.55 0.2226 0.22062 0.2178 0.25907 0.2524 RANDOM 15.59
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.29 1.89 -2.45 2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.621 r_dihedral_angle_4_deg 18.352 r_dihedral_angle_3_deg 15.898 r_scangle_it 11.115 r_scbond_it 6.604 r_dihedral_angle_1_deg 5.521 r_mcangle_it 4.814 r_mcbond_it 2.359 r_angle_refined_deg 0.966 r_chiral_restr 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.621 r_dihedral_angle_4_deg 18.352 r_dihedral_angle_3_deg 15.898 r_scangle_it 11.115 r_scbond_it 6.604 r_dihedral_angle_1_deg 5.521 r_mcangle_it 4.814 r_mcbond_it 2.359 r_angle_refined_deg 0.966 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10810 Nucleic Acid Atoms Solvent Atoms 575 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling